Polygenic Score (PGS) ID: PGS002060

Predicted Trait
Reported Trait Nasal polyps
Mapped Trait(s) Nasal polyposis (HP_0100582)
Additional Trait Information respiratory
Released in PGS Catalog: Jan. 10, 2022
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PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name portability-ldpred2_471
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 553,242
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
East Asian: 30%
European: 30%
African: 20%
Greater Middle Eastern: 10%
South Asian: 10%
10 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 391,124 individuals European UKB — — — UK (+ Ireland) —

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM011342 PSS009323|
European Ancestry|
19,106 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Nasal polyps — — Partial Correlation (partial-r): 0.0508 [0.0366, 0.0649] sex, age, birth date, deprivation index, 16 PCs —
PPM011343 PSS009097|
European Ancestry|
3,952 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Nasal polyps — — Partial Correlation (partial-r): 0.059 [0.0278, 0.0901] sex, age, birth date, deprivation index, 16 PCs —
PPM011344 PSS008651|
European Ancestry|
6,357 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Nasal polyps — — Partial Correlation (partial-r): 0.0441 [0.0195, 0.0686] sex, age, birth date, deprivation index, 16 PCs —
PPM011345 PSS008425|
Greater Middle Eastern Ancestry|
1,114 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Nasal polyps — — Partial Correlation (partial-r): 0.0084 [-0.0509, 0.0676] sex, age, birth date, deprivation index, 16 PCs —
PPM011346 PSS008205|
South Asian Ancestry|
6,007 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Nasal polyps — — Partial Correlation (partial-r): 0.0332 [0.0079, 0.0585] sex, age, birth date, deprivation index, 16 PCs —
PPM011347 PSS007987|
East Asian Ancestry|
1,740 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Nasal polyps — — Partial Correlation (partial-r): 0.0075 [-0.0398, 0.0547] sex, age, birth date, deprivation index, 16 PCs —
PPM011348 PSS007770|
African Ancestry|
2,365 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Nasal polyps — — Partial Correlation (partial-r): -0.002 [-0.0425, 0.0385] sex, age, birth date, deprivation index, 16 PCs —
PPM011349 PSS008874|
African Ancestry|
3,758 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Nasal polyps — — Partial Correlation (partial-r): -0.0088 [-0.0409, 0.0233] sex, age, birth date, deprivation index, 16 PCs —
PPM022198 PSS011841|
East Asian Ancestry|
5,885 individuals
 PGP000690 |
Jiang RS et al. Biomedicines (2023)
|Ext.		 Reported Trait: Chronic rhinosinusitis — AUROC: 0.534 [0.508, 0.56] — — —
PPM022202 PSS011842|
East Asian Ancestry|
535 individuals
 PGP000690 |
Jiang RS et al. Biomedicines (2023)
|Ext.		 Reported Trait: Nasal polyps in individuals with chronic rhinosinusitis — AUROC: 0.588 [0.537, 0.64] — — —
PPM022204 PSS011841|
East Asian Ancestry|
5,885 individuals
 PGP000690 |
Jiang RS et al. Biomedicines (2023)
|Ext.		 Reported Trait: Chronic rhinosinusitis — — Odds ratio (OR, high vs low PGS quartile): 1.477 [1.142, 1.91] — —
PPM022206 PSS011842|
East Asian Ancestry|
535 individuals
 PGP000690 |
Jiang RS et al. Biomedicines (2023)
|Ext.		 Reported Trait: Nasal polyps in individuals with chronic rhinosinusitis — — Odds ratio (OR, high vs low PGS quartile): 2.318 [1.371, 3.921] — —

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS008425 — — 1,114 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009097 — — 3,952 individuals — European Poland (NE Europe) UKB —
PSS008651 — — 6,357 individuals — European Italy (South Europe) UKB —
PSS009323 — — 19,106 individuals — European UK (+ Ireland) UKB —
PSS008205 — — 6,007 individuals — South Asian India (South Asia) UKB —
PSS008874 — — 3,758 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007987 — — 1,740 individuals — East Asian China (East Asia) UKB —
PSS007770 — — 2,365 individuals — African American or Afro-Caribbean Carribean UKB —
PSS011841 — —
[
  • 535 cases
  • , 5,350 controls
]
 — East Asian
(Taiwanese)		 — TPMI —
PSS011842 — —
[
  • 172 cases
  • , 363 controls
]
 — East Asian
(Taiwanese)		 — TPMI —